CM - I couldn't even begin to list them........ *G*. I had a shop for 20 years and over that much time I did a huge ammount of specialty work on Hot Rods Customs and Exotics. I'd be happy to help you plan this. This is as far as I've got:
In metal the Cougar and Mustang fastback are actualy way off. The cougar is longer by about 3" between the B post and the wheelwell, and the trunk width is 2" narower and 3" longer. It's not going to be one of those "just cut the roof at the A pillers and top of the 1/4's and weld it in" kind of jobs. The fasback section would need to be cut into at least 3 peices and lengthened which would change the shape also.
The most realistic way to do the job IMHO would be to do it in reverse. If a guy could find a 67/68 fastback mustang shell and swap the cougar sheetmetal onto it he would be way ahead to start. The doors are the same length, the deck width problem could be lost in the graft at the top of the 1/4's, the cowl and engine box section are the same so the whole front clip could be swapped. You would have to take 3" off the front of the cougar 1/4's at the front edge but that's do-able.
Before you start cutting up cars take a good long look at if it's worth it when you are done. I didn't think the cougar fastback realy looked that good, and for the same work and money you could build the cougar AND the fastback mustang into awesome cars in their own right and have both cars.